You were right. It really was a scaling issue. At first I imported the glyphs with 1/4 the size of the actual x-hight in Type3.2 and the problem occured. I dont know much about .svg files but there must be either a writing or reading issues with drawings that are too small.
Now if I scale the glyphs up in Illustartor and then import them to Type 3.2 everything seems to be fine.